His Betrayal
by SirKriS
Summary: Molly confronts Khan on the Enterprise as he is about to escape to his starship the Vengeance. Will Molly choose love or the law?
1. Chapter 1

**Author's Note: _So...this is my first fan fic, like ever. I'm not a very good writer but I had a lot of Khanolly feels (and strong tea) last night so I decided to brave up and write something. I was in the mood for some bitter-ish angst. Feel free to critique the heck out of it, I will glady welcome constructive advice. If I'm lucky, I might learn something and improve my writing :)_**

**_I do not own any characters I've written here._**

**_Enjoy!_**

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Khan ran through the halls of the enterprise, looking for a capsule exit to return to _Vengeance_, where his fellow augments would be waiting for him. He would have to make a stop back to Earth to recover Molly before they left for the other end of the galaxy. _'Molly'_ he thought; he hadn't seen her since he set his revenge plans in motion. In his passion to warrant a slow and brutal death to Admiral, Khan had overstayed his welcome on the _Enterprise_, which was now on full lockdown. Kirk and his insufferable crew will not hesitate to capture him now. Khan was just about to punch in an override code to access an unattended capsule when he heard a phase pistol charging up to fire a few feet behind him.

"You can't escape." The familiar voice constricted his chest as he turned to face the source. "The entire ship is on lockdown and I corrupted the code system anyway." Molly smiled humorlessly.

Khan he stared at the barrel pointed at his chest. He took a second to marvel at her steady aim, having never seen wield anything other than a medical instrument before. But wait, why was she on the _Enterprise_?

"Molly-" Khan began in a concerned voice.

"Don't" she shut her eyes painfully as his endearing voice released a flush of unwanted memories. Happy memories. She hadn't heard his smooth voice since that night he kissed her goodbye. Not since night before she woke up to see his face plastered across the federation, reporting him to be a wanted terrorist.

Khan stiffened in alarm. Something was wrong. He took a moment to roam his eyes across her attire and his face. Odd. She wasn't wearing her Starfleet medical uniform, instead it was a floral dress, though it looked slightly battered. Her wrists showed signs of bruises (most likely from repeated struggles) with numerous punctures on the side of her neck, not dissimilar to victims of the interrogation chair or truth serum. His face paled as he realized that Marcus must have had her interrogated to find his whereabouts. _'Bastard' _he thought._ 'I should have dismembered him more slowly'_ he thought darkly. Concerned rushed over him again as he focused back to Molly.

"I'm fine. Please don't pretend to care what happened to me. Not that it compares to what you did," she rushed to say when she realized he had deduced her appearance.

Being arrested on suspicion of collaboration, and the hellish events following after didn't affect her as much as his betrayal had on her broken heart, or her role in the Kelvin Archive explosions. Though the week-long solitary confinement nearly drove her mad thinking about him.

Her harsh words took him by surprise. Only then did he realize the consequences his deceit may have had on her perspective of him; _'On our relationship'_ he thought in dismay.

"You used me to get to Harewood—_lied_ to me—God, killed all those people" she choked out, trying not to let a sob escape. "I've alerted the crew. Kirk and the rest will be here for you any minute now. It's over _Khan_." His name tasted bitter as she addressed him by his real name. She still couldn't believe she fell in love with the worst terrorist the Federation had to face in over a century.

The Molly in front of unnerved him. He could tell she was serious. Her cheerful and carefree disposition was nowhere to be found in her eyes. "Molly—" he tried again, taking cautious but deliberate steps towards her.

"It's set to kill" she interrupted with deadly calm. She would have marveled at her strength had she not been so distracted by her internal turmoil.

Khan stopped at her words, a look of utter shock on his face. A rush of emotions played through his eyes; Molly could have sworn there was a flicker of—_'What, sadness? Hurt? Impossible,'_ she scolded herself. _'And how dare he. He's the one who betrayed me." _ By then Khan had recovered and resumed his steps, head cocked dangerously to the side as his eyes narrowed at her.

"I would be surprised if you did. You knew me to be a dangerous man well before and yet you still chose me." He smirked as he watched Molly's hand begin to tremble.

"I chose John, not you" she spat, his words were unraveling her and Molly could feel her resolve falter. It was getting harder to aim the pistol at him. She cursed her body's betrayal as tears also fell down her face.

Deep down he knew he shouldn't follow through with what he was going to say to her. He should work to find another way to appease her heart. But Khan was selfish and preferred to conquer rather than submit to raw sentiment.

"Do not delude yourself. John and I are one and the same. But do enlighten me," he pushed on, taking another deliberate step towards her, "is it my crimes you despise so much as your self-loathing capacity to love a murderer like me?"

"Just, stop it" she hissed. "I love—_loved_ you and you manipulated me." Was anything even true? No, don't answer that. I know you don't" she shook her head sadly.

Khan's smirk dropped as he observed her dejection. She truly thought she didn't matter. She was retreating from him emotionally and he didn't know what to say to get her back.

"Our attraction was under no manipulation." _'I'm sorry. I love you'_ he wanted to say. Why can't he say it? "I chose you as sincerely as you did me. Khan felt frustrated as he tried to explain himself. _'Cursed sentiment.'_ Even in the face of losing her, he wouldn't give into it entirely.

"Marcus was as much a traitor to your Federation as he was to my family. Those deaths were a necessary means to a justifiable end. Even you cannot condone the severity of his actions. Don't you see?" _'I would kill for you.'_

"Necessary" she scoffed incredibly. Her hope for them had flared in her heart, only to fall as he casually dismissed his crimes. It was alright if he wouldn't love her. But the moment he dismissed innocent life would be where he crossed a line.

She loved him, but he was a criminal. She couldn't forgive him. She wouldn't.

With that sobering thought Molly's resolve returned at full force. She used her other hand to steady the weapon and aimed it over his heart. Only then did she realize how much he had advanced towards her.

"Don't make another move. I will not hesitate to shoot you."

He was a foot away from the end of her pistol, the distance slowly closing between them.

"I swear, I will kill you" a fresh wave of tears blurred her vision but she remained steady.

Khan took another step towards her, his features softening.

"No, you won't Mrs. Harrison" he said quietly.

Molly released a breath she did not realize she had been holding and with a heavy heart, pulled the trigger.

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**Author's Note:** _Oh and for maximum visual feels, check out this fanvideo: watch?v=QeEwA1P8Z5E _

_It kind of inspired me to write the story._


	2. Chapter 2

**Author's Note: Sorry it took a while to update this one. I needed to figure what development to go through with (I had too many after the last chapter).  
**

**Still very angsty. Hope you like it :)**

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Khan's eyes widened in pain before he crumpled to the ground. Kirk, Spock, and McCoy arrived as Molly's arms fell limply to her sides. Kirk stared at Khan's motionless body then back at Molly's phase pistol before looking up at he to ask

"Did you—"

"No."

Molly flipped the pistol in her hand to hold the barrel and handed the weapon to Kirk.

"It's a modified phase pistol I stole from Marcus' office earlier. I used the stun setting on him but the megajoules capacity is higher so it may take him a while to regain consciousness."

Kirk was about to ask something when Spock interrupted asked.

"Molly are you alright? We found out Marcus was keeping you in the interrogation room."

McVoy, who had been inspecting Khan turned back suddenly at that.

"What?!" He rushed to her side to examine her and hissed slightly when he saw the puncture wounds on her neck.

"Bones, I'm fine. They're from the truth serums, really." Molly smiled assuredly. She flinched slightly as his touch brought up unpleasant memories of her interrogation but forced back her smile. "I don't have any physical injuries to worry about."

McCoy was about to argue when she said, "You're not the only one who graduated from medical school remember?" Although he wasn't convinced she was okay, McCoy's mouth quirked up to a smile.

"Okay, but at least go get some rest," he insisted.

"Oh, you don't need to tell me twice. On my way." She gave a playful salute as she passed the men, making sure not to look at the man on the floor.

Kirk had narrowed his eyes at her cheerful demeanor but chose not to comment. It was obvious that Molly didn't want to Molly's back retreated behind a corner Spock turned to Kirk.

"I think she's a lot more hurt than she wishes to divulge." To clarify his point he motioned towards the unconscious Khan.

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Molly tried her best not to break down as she walked down the halls. She just needed to get back to her quarters, then she could relax. Almost there, she encouraged herself. Relief washed over her when she realized that her roommate wasn't in. Given the chaos Khan had stirred up on the Enterprise, she didn't think anyone would want to stay on the vessel much longer anyway.

Khan.

Tears began to fall at the thought of him. She let the sobs rack her body as she slowly made her way to the bed. Her life had spiraled into a living hell after meeting John—Khan. Molly smiled bitterly to herself at her mental slip up.

"I hate him," she whispered to herself until she let exhaustion take over.

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Khan woke up to find himself back in the transparent brig. The last thing he could recall was the pistol's low hum as Molly reset it before firing at him. Though grateful she changed her mind, he knew it wouldn't be enough to get her back. He rubbed an arm over the spot Molly had hit. His augment properties may have hastened his recovery but his chest still hurt at the thought of her.

He sat up abruptly when he realized someone was observing him. He turned towards the barrier to find Kirk.

Khan smirked up at him. "I take it you're here to rejoice my captivity, though you must be disappointed you didn't achieve it yourself."

Kirk folded his arms as he chose to ignore the bait. "You know you won't see her again."

Khan's eyes flashed slightly as he got up slowly to walk towards the man.

"Not unless she wants to see you of course; which probably won't happen."

"Oh?" He raised an eyebrow. "Pray tell, why you're so certain."

"You should know. You're the one who betrayed her."

Khan stiffened.

Kirk registered the reaction before he shrugged. "Anyway, not that it matters to you. She was just a pawn in your grand scheme for revenge."

A muscle twitched on his otherwise calm exterior. He knew what Kirk was trying to do.

Khan walked until he was mere centimeters away from the barrier. "You would have done the same for your family."

Kirk nodded thoughtfully. "You're right. I might do anything for my family. But you forget Khan," he said, approaching closer to the barrier. "She was your family too."

Deadly silence followed after as the two men glowered at one another until Kirk finally broke the eye contact.

"You shouldn't have used her," was all he said before leaving Khan's sight.

Silver waves rippled across the surface as Khan punched the barrier again and again. He didn't stop until he felt the fractures form. His head slumped as a tear escaped his eye.

"Molly…"

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**Author's Note: Not sure how many many more chapters will follow. I may know for sure after the next chapter.**

**Thank you for reading!**


	3. Chapter 3

Molly got up feeling rather numb all over. She rubbed the dry trails of tears on her cheeks before getting slowly and to look across the room. Still no roommate; maybe she got evacuated after all.

"Morning sunshine."

Molly turned towards the door. Kirk was leaning on the door frame with his arms folded.

"What time is it?" she croaked.

He looked down at his watch. "Well it's 8am right now. But you've been sleeping for 3 days. Bones was almost sure you fell into a coma."

Molly groaned and covered her face "Ugh, I must look awful."

Kirk nodded seriously. "You could say that." Molly chuckled softly. "How do you feel?"

She smiled. "I'm fine. Just a little sore all over. Slept too much I guess." She sat up further and noticed the tray of breakfast by the bedside.

"I hope you still like chocolate pancakes. You used to love them when we were kids." Kirk smiled. "I know they're not my mom's but hey, I tried."

She raised an eyebrow. "You made this?" Kirk scratched his head. "Yeah, but I might have had a little help," he said nervously. Molly bit into a pancake and made a show of chewing it with criticism.

He huffed at her antics "I tried it too, you know." She put her finger up to silence him and scrunched up her face at him. After an audible swallow she grinned up at him.

"It's absolutely edible," she grinned up at he when he rolled his eyes at her. The room fell into comfortable silence as Kirk watched Molly eat.

"Molls..." he started.

"I said I'm fine James." She immediately winced; she knew he was just worried. "Sorry I'm just…tired is all."

Kirk nodded before sighing. He really didn't want to tell her, but he preferred she heard it from him.

"His verdict is out."

Her body tensed in anticipation as the next words followed.

"They're putting him back to cryosleep."

She shut her eyes, hating how relieved she was to know he wasn't going to die, even after everything.

"When? And how long?"

"Tomorrow at noon. Technically he's to be in stasis indefinitely, but he may be revived after 150 years."

"A lifetime," she said quietly.

Kirk looked at her carefully. He knew she was hurting, but it was clear she didn't want to open up to him, not yet at least.

"Are you going to go see him? Before…" his words trailed off when Molly threw him an infuriated look. "Alright," he put his arms up, "look, just hear me out. I don't care about the bastard, and frankly I don't want you anywhere near him again, but he's not just a criminal is he? And you two have unfinished business." She was still glaring at him.

"Molls," he said softly, "I want you to be fine after he's gone too."

She deflated slightly, looking down.

"I know."

Kirk stood uncertainly by the door before walking up to sit by her.

"Don't keep it all in. You don't have to feel alone, ever. You hear me?" He reached out to draw he hair from her face and hissed when he saw her neck.

"Bones might be right about that check up. Are the punctures supposed to look like that?"

Molly touched her neck reflexively."Why, are they purple?" He nodded, a look of slight panic on his face.

"Oh. I bruise easily that's all. They weren't exactly done by a medic" she joked.

"Don't joke about that." Kirk looked really concerned. "You still haven't gone to the medical bay since you got out. Never mind," he got up to leave. " I'm getting Bones right now."

"Is Bones finally rubbing off on you?" she teased. Kirk was infamous for dismissing medical attention. He sat back down and looked at her confused before breaking into a smile. "Shut up." Molly giggled.

"I'll clean myself up and go see Bones right after," he eyed her warily. "I _promise_. Now can you stop fussing? I know the ship can fly on it's own but you really

should get back to the bridge now."

He lingered for a moment, then got up to leave. He turned back one more time to say something when she interrupted

"I'll even tell Bones you're the one who convinced me to go." She winked at him "You know, that's no small feat."

"Right," he chuckled at that. "See you soon then." He saw her wave cheerfully before the door shut between them.

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Kirk made it all the way back to the control room before he realized that his cousin never answered him.

"Damn it, Molly."

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**A/N: Sorry, no Khan in this chapter but he will be back in the next one.**


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